In-Cell Dynamics: The Next Focus of All-Atom Simulations

Premila P. Samuel Russell, Sepehr Alaeen, Taras V. Pogorelov

Research output: Contribution to journalReview articlepeer-review

Abstract

The cell is a crowded space where large biomolecules and metabolites are in continuous motion. Great strides have been made in in vitro studies of protein dynamics, folding, and protein-protein interactions, and much new data are emerging of how they differ in the cell. In this Perspective, we highlight the current progress in atomistic modeling of in-cell environments, both bacteria and mammals, with emphasis on classical all-atom molecular dynamics simulations. These simulations have been recently used to capture and characterize functional and non-functional protein-protein interactions, protein folding dynamics of small proteins with varied topologies, and dynamics of metabolites. We further discuss the challenges and efforts for updating modern force fields critical to the progress of cellular environment simulations. We also briefly summarize developments in relevant state-of-the-art experimental techniques. As computational and experimental methodologies continue to progress and produce more directly comparable data, we are poised to capture the complex atomistic picture of the cell.

Original languageEnglish (US)
Pages (from-to)9863-9872
Number of pages10
JournalJournal of Physical Chemistry B
Volume127
Issue number46
DOIs
StatePublished - Nov 23 2023

ASJC Scopus subject areas

  • Materials Chemistry
  • Surfaces, Coatings and Films
  • Physical and Theoretical Chemistry

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